removeSpots            package:arrayMagic            R Documentation

_R_e_m_o_v_e _s_p_e_c_i_f_i_e_d _s_p_o_t_s _f_r_o_m _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     All elements matching the strings in 'spotsToBeRemoved' are taken
     out of the object 'arrayDataObject' and  the corresponding ones
     out of the object 'exprSetRGObject' as well, if supplied.

_U_s_a_g_e:

     removeSpots(arrayDataObject, exprSetRGObject=NULL, spotsToBeRemoved=NULL, spotIdentifier="Name")

_A_r_g_u_m_e_n_t_s:

arrayDataObject: object of type 'arrayData'; required; default: missing

exprSetRGObject: object of type 'exprSetRG'; optional; default: 'NULL'

spotIdentifier: character string, i.e. name of the column of
          'getSpotAttr(arrayDataObject)' used for matching; default
          "Name"

spotsToBeRemoved: vector of character strings; default: 'NULL'

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     A named list containing an object of type 'arrayData' labelled
     "arrayDataObject", an object of type 'exprSetRG' labelled
     "exprSetRGObject" and an integer specifying the number of removed
     items labelled "nrOfRemovedItems".

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'arrayData-class', 'exprSetRG-class'

_E_x_a_m_p_l_e_s:

       intensities <- array(data=runif(600),dim=c(100,2,3))
       dimnames(intensities) <- list(NULL, c("green","red"), NULL)
       arrayDataObject <- new("arrayData", intensities=intensities, spotAttr=data.frame(Name=I(rep(c("x","y","Blank","Blank","z"),20))), hybAttrList=NULL)
       res <- removeSpots(arrayDataObject, spotsToBeRemoved=c("x","z"))
       stopifnot( dim(getIntensities(res[["arrayDataObject"]]))[1] == 3*20 )

        
       

